I have a Chrome Extension that does a window.open() when the extensions icon is clicked. (It can\'t use the traditional Chrome extension popup due to an unrelated bug in Chrome)
Instead of using window.open() use the Chromes chrome.windows.create... http://code.google.com/chrome/extensions/windows.html#method-create
...then in the call back you can record its window.id and then any time you want to make it focused you can use chrome.windows.update.